Epigenetic signals, p-values This composite track, "Signal p-values", provides access and visualization to the normalized epigenetic signals as p-values for deviation from expectation of a negative binomial distribution.
In "dense" mode, the display gives a compact view of the level of epigenetic signal for each feature in each cell type. In "full" mode, the normalized signal strength is shown as a continuous, variable signal. Users have options for setting the y-axis on the Track Settings page of each composite track.
The track names (short name and the end of the long name) give an abbreviation for the blood cell type and the biosamples from the Blueprint Consortium (replicates are from different donors) or the file id after downloading and processing other published data (100xxx). The cell types are HSC = hematopoietic stem cell, MPP = multipotent progenitor cell, LMPP = lymphoid-myeloid primed progenitor cell, CMP = common myeloid progenitor, MEP = megakaryocyte erythrocyte progenitor, GMP = granulocyte monocyte progenitor, CLP = common lymphoid progenitor, CD34_E = erythroblasts generated by in vitro differentiation of CD34+ HSCs, ERY = erythroblast, MK = megakaryocyte, EOS = eosinophil, MONp = primary monocyte, MONc = classical monocyte, NEU = neutrophil, B = B cell, NK = natural killer cell, T_CD4 = CD4+ T cell, T_CD8 = CD8+ T cell, HUDEP = immortalized human umbilical cord blood—derived erythroid progenitor cell lines expressing fetal globin genes (HUDEP1) or adult globin genes (HUDEP2), K562 = a human cancer cell line with some features of early megakaryocytic and erythroid cells. AVE is a track with state assignments based on the average signal for each epigenetic feature across cell types.
The genome-wide signals for the epigenetic features were normalized across cell types using the S3V2 version of S3norm in the pipeline S3V2-IDEAS (Xiang et al. 2020 and 2021). The S3V2 method was developed to normalize the signal to bring out peaks without inflating the background while also denoising the data.
The data normalization was done by Guanjue Xiang. The data downloads, re-mapping and processing, generation of the tracks displayed, and development of the track hub were done by Belinda Giardine.
Xiang G, Keller CA, Giardine B, An L, Li Q, Zhang Y, Hardison RC. S3norm: simultaneous normalization of sequencing depth and signal-to-noise ratio in epigenomic data. Nucleic Acids Res. 2020 May 7;48(8):e43. doi:10.1093/nar/gkaa105. PMID: 32086521; PMCID: PMC7192629.
Xiang G, Giardine BM, Mahony S, Zhang Y, Hardison RC. S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types. Bioinformatics. 2021 Sep 29;37(18):3011-3013. doi:10.1093/bioinformatics/btab148. PMID: 33681991; PMCID: PMC8479670.
These data are available for use without restrictions.